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Billie J. Swalla
Transcriptome Sequencing Reveals Heterochronic Shift of
Chordate Gene Networks in Molgulid Ascidians
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Tunicates
Ambulacraria Chordata
Cephalochordates
Modified from
Swalla et al. 2001
Xenoturbella
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Heterochronyhttp://www.bio.miami.edu/dana/dox/heterochrony.html
Allometric Growth Differential growth in organs and body parts
PaedomorphyRetention of juvenile structures
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Heterochronyhetero = otherchronos = time
Haekel – 1875de Beer – 1930 “Embryos and Ancestors”
Gould – 1997 “Ontogeny and Phylogeny”
“Few Evolutionary concepts have generated more confusion and controversy than heterochrony” McKinney, 1999
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C. Titus Brown
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Evolution and Development of Tailless Ascidians
1. Changes in gene expression in regulatory genes
2. Downstream structural genes become pseudogenes (muscle)
3. Heterochrony - changes in timing of gene activation
4. Gene Loss
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Molgula clades
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Solitary ascidians have determinant
and invariant cleavage.
Some species have colored cytoplasms.
(Boltenia villosa)
The cell lineage is very similar in Ciona, Phallusia,
Halocythia roretzi &Molgula oculata.
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Two Species of Closely Related Ascidians and a Hybrid Larva
Molgula oculata has a head, tail, and otolith - chordate embryo.
M. occulta egg X M. oculata sperm has a head, short tail, and otolith.
Molgula occulta lacks chordate features - head, tail, and otolith.
Swalla and Jeffery, 1996
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Notochord formation (convergence & extension)
Jiang and Smith, 2007
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Notochord Gene Network
Davidson and Christiaen, Cell (2006)
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Molgula oculata notochord(40 cells, converged & extended)
Molgula occulta no notochord(20 cells, not converged & extended)
Hybrid notochord(20 cells, converged & extended)
Notochord Formation in Molgulids
Swalla and Jeffery, 1996
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Digital normalization
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Digital normalization
Lowe, Swalla, Brown, in preparation
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Digi Norm assembly vs Raw read assembly
37 1713623
Digi Norm Raw
2446C. intestinalis
M. occulta
64 1513646
Digi Norm Raw
2398C. intestinalis
M. oculata
Lowe, Swalla, Brown, in preparation
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Stage specific express
Lowe, Swalla, Brown, in preparation
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Notochord gene expression similar to tailed species
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Prickle
Veeman, M., et al., 2007
•Planar cell polarity (PCP) pathway
•Involved in convergence and extension
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Prickle expressed in notochord cells
Mita et al Zool. Sci., 2010
M. occulta gastrulation Ciona intestinalis
Satoh Nature Reviews Genetics 4, 2003
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Hybrid notochord genes allele specific differential express
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Notochord Gene Network
Davidson and Christiaen, Cell 2006
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Ascidian Metamorphosis
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Heterochronic shift of metamorphosis genes in Molgula
Gene Species Cleavage
Gastrula/Neurula
Tailbud Larva Juvenile
META-2 C. intestinalis
M. oculata
M. occulta
M. tectiformis
Echinonectin C. intestinalis
M. oculata
M. occulta
M. tectiformis
50/168 genes show early differential expression in Molgula compared to C. intestinalis
Larval development
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Ascidian Development
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Heterochronic Shift inMolgulidae Development
*79 genes examined across of six species
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Billie Swalla, Nadine Peyrieras, Alberto Stolfi
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M. occulta F+ 12 hatching
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M. occulta transgenic NoTrlc Alberto Stolfi & Lionel Christiaen
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Summary
Both tail and tailless species contain the majority of known notochord genes
Digital Normalization performs as well or slightly better than raw read assembly
Metamorphosis genes are expressed much earlier than in other ascidian species
Early onset of Metamorphosis may be a pre-adaptation to evolution of a tailless embryo
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Thanks to Beacon!!
1. Great colleagues!!2. Revived an exciting research
program that benefited greatly from genomics methods
3. Leadership opportunities and support for female faculty
4. Graduate student support for travel and courses.
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2012 Swalla Lab
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Acknowledgements
University of Washington Michigan State University
• Dr. Titus Brown
• Dr. Kanchan Pavangadka
• Elijah Lowe
• Dr. Billie J. Swalla
• Dr. Charlotte Konikoff• Kristin Andrykovich • Kelly Hennessey• Max Maliska• Lauren Vandepas New York University
Dr. Lionel Christiaen
Dr. Alberto Stolfi
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96/98 Sanger-sequenced Molgulid genes contained by global assembly.
69% of M. oculata transcripts found (BLASTX 1e-12) in Ciona proteome.
55% of M. occulta transcripts => Ciona.
How do we evaluate assembly?
Query: 1MDSSNRSHPNAHLQYHTDYNYPPFRRVMLAAVKEGLYHPRLPSLRRMDMDTATHKLPDEH 60 MDSSNRSHPNAHLQYHTDYNYPPFR+VMLAAVKEGLYHPRLPSLRRMDMDTATHKLPDEHSbjct: 50MDSSNRSHPNAHLQYHTDYNYPPFRKVMLAAVKEGLYHPRLPSLRRMDMDTATHKLPDEH 229
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Mapping => quantitation
Reference transcriptome required.
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Assembly contig lengths
M. oculata M. occulta
Lowe, Swalla, Brown, in preparation
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Tailless allele has high expression in hybrids PCP
pathway